Misunderstandings about isochores: A review

Giorgio Bernardi
Stazione Zoologica Anton Dohrn
Villa Comunale 80121 Napoli
Italy
telephone: 0039 081 5833300
fax: 0039 081 2455807
email: bernardi@alpha.szn.it
prestype: Platform
presenter: Giorgio Bernardi

Giorgio Bernardi

Laboratorio di Evoluzione Molecolare
Stazione Zoologica Anton Dohrn
Napoli 80121
Italy

The draft sequence paper published by the International Human Genome Sequencing Consortium (IHGSC) is different from previous sequence reports (including the paper published simultaneously by Venter et al., 2001), which presented data and addressed issues of sequence analysis and gene prediction, in that the IHGSC attempted to also present a general picture of a very broad and complex research area, that of the organization and evolution of the human genome. This attempt was apparently too ambitious, also in view of the time and space limitations imposed on the authors. As a consequence, some erroneous and controversial conclusions found their way into the paper. Since, in all likelihood, the IHGSC article will have a very wide circulation, it is important that such conclusions be corrected or critically discussed before they spread into the literature and become (at least temporarily) established truths. This discussion of the IHGSC paper is, in fact, already under way on some of the topics addressed. For instance, the proposed horizontal transfer of bacterial genes to vertebrates was shown to be explained, in most cases, by descent through common ancestry (Stanhope et al. 2001; Roelofs and Van Haastert, 2001). Here, the discussion will be focused on some subjects of the IHGSC paper previously dealt with in our laboratory, such as the broad genomic landscape, namely the isochore pattern of the human genome, the distribution of repeats and genes in the isochores, and the mutational bias, i.e. the non-randomness of the mutational input.